5-56796952-T-A

Position:

• chr5-56796952-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.636 in 151,866 control chromosomes in the GnomAD database, including 31,693 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31693 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96505 AN: 151748 Hom.: 31675 Cov.: 30

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.641

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.636 AC: 96555 AN: 151866 Hom.: 31693 Cov.: 30 AF XY: 0.627 AC XY: 46503 AN XY: 74224

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.636

Alfa AF: 0.664 Hom.: 4248

Bravo AF: 0.618

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3309; hg19: chr5-56092779;